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Two-level domain decomposition preconditioner for 3D flows in anisotropic highly heterogeneous porous media is presented. Accurate finite volume discretization based on multipoint flux approximation (MPFA) for 3D pressure equation is employed to account for the jump discontinuities of full permeability tensors. DD/MG type preconditioner for above mentioned problem is developed. Coarse scale operator is obtained from a homogenization type procedure. The influence of the overlapping as well as the influence of the smoother and cell problem formulation is studied. Results from numerical experiments are presented and discussed.